X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqVector.java;h=763206702d3cf7c7e591dc1b65d82a14ecdb207c;hb=0353fb50f77f7d60e3c88c297298d04e0b1b80b3;hp=9a98f3e8448336c948a975f9b2ed45eef45efc89;hpb=c762d9525db36ffd5d3fca49fb5e7d506d13401a;p=jalview.git
diff --git a/src/jalview/ws/rest/params/SeqVector.java b/src/jalview/ws/rest/params/SeqVector.java
index 9a98f3e..7632067 100644
--- a/src/jalview/ws/rest/params/SeqVector.java
+++ b/src/jalview/ws/rest/params/SeqVector.java
@@ -1,23 +1,47 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ *******************************************************************************/
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.Option;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
+import jalview.ws.rest.RestServiceDescription;
import jalview.ws.rest.InputType.molType;
import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.StringBody;
+import org.jmol.util.ArrayUtil;
/**
* input a list of sequences separated by some separator
* @author JimP
*
*/
-class SeqVector extends InputType {
+public class SeqVector extends InputType {
String sep;
molType type;
public SeqVector()
@@ -40,4 +64,65 @@ class SeqVector extends InputType {
}
return new StringBody(idvector.toString());
}
+ @Override
+ public List getURLEncodedParameter()
+ {
+ ArrayList prms = new ArrayList();
+ super.addBaseParams(prms);
+ prms.add("sep='"+ sep+"'");
+ if (type!=null)
+ {
+ prms.add("type='"+type+"'");
+ }
+ return prms;
+ }
+
+ @Override
+ public String getURLtokenPrefix()
+ {
+ return "SEQS";
+ }
+
+ @Override
+ public boolean configureProperty(String tok, String val,
+ StringBuffer warnings)
+ {
+
+ if (tok.startsWith("sep"))
+ {
+ sep=val;
+ return true;
+ }
+ if (tok.startsWith("type"))
+ {
+ try {
+ type=molType.valueOf(val);
+ return true;
+ } catch (Exception x)
+ {
+ warnings.append("Invalid molecule type '"+val+"'. Must be one of (");
+ for (molType v:molType.values())
+ {
+ warnings.append(" "+v);
+ }
+ warnings.append(")\n");
+ }
+ }
+ return false;
+ }
+
+ @Override
+ public List getOptions()
+ {
+ List lst = getBaseOptions();
+ lst.add(new Option("sep",
+ "Separator character between elements of vector", true, ",",
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type,
+ molType.MIX));
+
+ return lst;
+ }
+
}
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